slides - Computer Science Department

Report
Scalable Distributed Fast
Multipole Methods
Qi Hu, Nail A. Gumerov, Ramani Duraiswami
Institute for Advanced Computer Studies
Department of Computer Science
University of Maryland, College Park, MD
1
Previous work
•
•
FMM algorithm for GPUs
-
Gumerov and Duraiswami (2008) explored the FMM algorithm for GPU
-
Yokota, et al. (2009) presented FMM on the GPU cluster
FMM algorithm for distributed systems
- Greengard and Gropp (1990) discussed parallelzing FMM
- Ying, et al. (2003): the parallel version of kernel independent FMM
- Lashuk, et al. (2009) presented kernel independent adaptive FMM on
heterogeneous architectures
- Cruz, et al. (2010): the PetFMM library
- Hu, et al. (2011): the heterogeneous FMM algorithm
- Yokota, et al. (2011): using FMM to simulate turbulence on 4096 GPUs
2
Issues with previous results
• Communication data structures: local essential tree
- Bottleneck
- No details of implementation
• Especially, our previous work Hu, et al. (2011):
- The L|L translations are not fully distributed
- Very large data transfer overheads
3
Contributions
• Efficient salable communication management data structures
- Classify the spatial boxes
- Determine boxes for internode exchange on GPU
- Only communicate necessary data
- Small amount of communication data
• Fully distribute the all parts of FMM among all the nodes
• Extremely fast parallel algorithms for FMM data structures
- Complexity O(N) and much faster than evaluation steps
- Suitable for dynamics problems
4
Motivation: Brownout
• Complicated phenomena involving interaction between rotorcraft
wake, ground, and dust particles
• Causes accidents due to poor visibility and damage to helicopters
• Understanding can lead to mitigation strategies
• Lagrangian (vortex element) methods to compute the flow
• Fast evaluation of the fields at particle locations
• Need for fast evaluation of all pairwise 3D interactions
5
Motivation
Many other applications require fast evaluation of pairwise
interactions with 3D Laplacian kernel and its derivatives
Astrophysics
(gravity potential
and forces)
Molecular Dynamics
(Coulomb potential
and forces)
wissrech.ins.uni-bonn.de
Micro and
Nanofluidics
(complex channel
Stokes flows)
Imaging and
Graphics (high
quality RBF
interpolation)
Much More!
6
Introduction to fast multipole methods
• Problem: compute matrix-vector product of some kernels
• Linear computation and memory cost O(N+M) with any accuracy
• Divide the sum to the far field and near field terms
• Direct kernel evaluations for the near field
• Approximations of the far field sum via the multipole expansions
of the kernel function and spatial data structures (octree for 3D)
7
Introduction to the fast multipole method
• The local and multipole expansions of the Laplace kernel at the
center
with the truncation number p
rnYnm local spherical
basis functions
r −(n+1)Ynm multipole spherical
basis functions
• Expansions regions are validated by well separated pairs realized
using spatial boxes of octree (hierarchical data structures)
• Translations of expansion coefficients
- Multipole to multipole translations (M|M)
- Multipole to local translations (M|L)
- Local to local translations (L|L)
8
FMM flow chart
1. Build data structures
2. Initial M-expansions
3. Upward M|M
translations
4. Downward M|L, L|L
translations
5. L-expansions
6. Local direct sum (P2P)
and final summation
From Java animation of FMM by Y. Wang M.S. Thesis, UMD 2005
9
Issues with distributed algorithms
• Halo regions
• Incomplete translations
10
Solutions
• Distribute the entire computing domain based on the
global workload balance
• Classify the spatial boxes into 5 categories
- Need to calculate box types efficiently
- No interruptions on kernel evaluations
• A single communication to exchange data of halo regions
- Master-slave model
- Small overheads
• All other computations are performed independently
- Fully distributed
11
Heterogeneous architecture
12
Mapping the FMM on CPU/GPU architecture
• GPU is a highly parallel, multithreaded,
Hundreds of cores
many-core processor
- Good for repetitive operations on multiple
data (SIMD)
• CPUs are good for complex tasks with
DRAM
GPU
- Complicated data structures, such as FMM
A few cores
M|L translation stencils, with complicated
patterns of memory access
Control
ALU
ALU
ALU
ALU
• CPU-GPU communications expensive
Cache
• Profile FMM and determine which parts
of FMM go where
DRAM
CPU
13
FMM on the GPU
• Look at implementation of Gumerov & Duraiswami (2008)
- M2L translation cost: 29%; GPU speedup 1.6x
- Local direct sum: 66.1%; GPU speedup 90.1x
• Profiling data suggests
- Perform translations on the CPU: multicore parallelization and large
cache provides comparable or better performance
- GPU computes local direct sum (P2P) and particle related work: SIMD
cost
100
80
speedup
60
40
20
0
M-expansion
M2M
M2L
L2L
L-expansion
Local direct
sum
14
Workload distribution
• A forest of trees
• Workload balance
15
The distributed FMM algorithm on a single node
16
The distributed algorithm on multiple nodes
17
A 2D example
18
Box types
• Five types: root, import, export, domestic, other
• Each node computes its box types on GPUs with
other FMM data structures
• Very small overhead
• A 2D example
19
Communication overhead
• Depend on the input data distribution
• It is proportional to
- the number of computing node P
- the number of boxes in the boundary (halo) regions
- Assume the uniform distribution
- Cost:
20
Comments on implementations
• Other FMM data structures (interaction lists) and
heterogeneous implementations
- Using the heterogeneous algorithms in Hu, et al. (2011)
• All data structures passed to the kernel evaluation engine
are compact, i.e. no empty box related structures
• The data manager is on the master node and implemented
on CPU
- Its workload is small
- No noticeable gain of its GPU implementation
21
Weak scalability
• Compare with Hu et al. (2011)
• Reduce both the overheads and kernel evaluations
• Fix 8M per node and run tests on 1 ~ 16 nodes
• The depth of the octree determines the overhead
• The particle density determines the parallel region timing
22
Weak scalability
23
Weak scalability
24
Strong scalability
• Fix the problem size to be 8M particles
• Run tests on 1 ~ 16 nodes
• Direct sum dominates the computation cost
- Unless GPU is fully occupied algorithm does not achieve
strong scalability
- Can choose number of GPUs on a node according to size
• Compare with Hu et al. (2011)
25
Strong scalability
26
Strong scalability
27
The billion size test case
• Using all 32 Chimera
nodes and 64 GPUs
• 230 ~1.07 billion particles
potential computation in
12.2 s vs 21.6 s in Hu et
al. (2011)
- 32 M per node
Each node:
Dual quad-core Intel
Nehalem
5560 2.8 GHz processors
24 GB of RAM
Two Tesla C1060 GPU
28
Performance count
HPCC 2012
SC’11
SC’10
Paper
Hu et al. 2012
Hu et al. 2011
Hamada and
Nitadori, 2010
Algorithm
FMM
FMM
Tree code
Problem
size
1,073,741,824
1,073,741,824
3,278,982,596
Flops count
39.7 TFlops
on 64 GPUs,
32 nodes
38 TFlops
on 64 GPUs,
32 nodes
190 TFlops
on 576 GPUs,
144 nodes
GPU
Tesla C1060:
1.296 GHz
240 cores
Tesla C1060:
1.296 GHz
240 cores
GTX 295
1.242 GHz
2 x 240 cores
620 GFlops/GPU
593 GFlops/GPU
329 GFlops/GPU
29
Conclusion
• Fast communication management data structures
- Handle non-uniform distribution
- Parallel granularity: spatial boxes
- Small overheads
• Much improved scalability and performance
• The capability of computing million or billion size problems
on a single workstation or a middle size cluster
• Developed code will be used in solvers for many large scale
problems in aeromechanics, astrophysics, molecular
dynamics, etc.
30
Questions?
Acknowledgments
31

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